Variant report

Variant	rs1002162
Chromosome Location	chr2:20656297-20656298
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
2	chr2:20654763..20657420-chr2:20673291..20675499,2	K562	blood:
3	chr2:20647398..20650409-chr2:20654175..20656821,4	K562	blood:
4	chr2:20655892..20657578-chr2:20694360..20697457,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118960	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10204085	0.92[JPT][hapmap]
rs10205221	0.85[CEU][hapmap]
rs1062292	0.87[CHD][hapmap]
rs10856799	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11898154	0.96[CEU][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs11901246	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12988451	0.85[CEU][hapmap]
rs13021908	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1453051	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168195	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872070	0.96[CEU][hapmap];0.81[CHB][hapmap];0.82[EUR][1000 genomes]
rs2084919	0.89[CEU][hapmap]
rs2348707	0.83[EUR][1000 genomes]
rs342105	0.82[GIH][hapmap]
rs342106	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342107	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342110	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs342111	0.90[EUR][1000 genomes]
rs342114	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342116	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342118	0.84[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs342123	0.81[CEU][hapmap]
rs342124	0.81[CEU][hapmap]
rs342126	0.81[CEU][hapmap]
rs4666308	0.85[CEU][hapmap]
rs4666396	0.93[CHD][hapmap];0.82[GIH][hapmap]
rs4666397	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4666398	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666401	0.96[CEU][hapmap];0.81[CHB][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs4666402	0.85[CEU][hapmap]
rs6531240	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6704834	0.84[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs674534	0.81[CEU][hapmap]
rs715670	0.85[CEU][hapmap]
rs7601359	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs959058	0.85[CEU][hapmap]
rs9917322	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455830	chr2:20621404-20659862	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv581166	chr2:20621404-20659862	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
3	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
8	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
9	nsv873722	chr2:20652507-20705910	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1002162	FAM49A	cis	cerebellum	SCAN
rs1002162	HS1BP3	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20650800-20659000	Weak transcription	Pancreas	Pancrea
2	chr2:20651400-20656600	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr2:20651600-20656600	Weak transcription	HSMM	muscle
4	chr2:20652400-20657000	Weak transcription	Osteobl	bone
5	chr2:20653000-20657600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:20653200-20666200	Weak transcription	Brain Anterior Caudate	brain
7	chr2:20653400-20666400	Weak transcription	Brain Substantia Nigra	brain
8	chr2:20653400-20674000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:20654000-20665400	Weak transcription	Brain Hippocampus Middle	brain
10	chr2:20654800-20657200	Enhancers	Stomach Smooth Muscle	stomach
11	chr2:20655600-20657400	Enhancers	Rectal Smooth Muscle	rectum
12	chr2:20655600-20657600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:20655800-20656400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:20655800-20656800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:20655800-20657200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:20655800-20657200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr2:20655800-20657600	Enhancers	Colon Smooth Muscle	Colon
18	chr2:20656000-20657000	Enhancers	NHDF-Ad	bronchial
19	chr2:20656000-20657200	Enhancers	NH-A	brain
20	chr2:20656000-20657200	Enhancers	NHLF	lung
21	chr2:20656000-20657400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:20656000-20658800	Enhancers	HepG2	liver
23	chr2:20656200-20657000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:20656200-20657200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr2:20656200-20657400	Weak transcription	Psoas Muscle	Psoas
26	chr2:20656200-20657600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr2:20656200-20658000	Weak transcription	Gastric	stomach
28	chr2:20656200-20658200	Weak transcription	Esophagus	oesophagus
29	chr2:20656200-20671800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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